/// <summary>
/// Gets Aligned seqeunces in the Specified SAM file.
/// </summary>
/// <param name="textReader">SAM file stream.</param>
private IEnumerable <SAMAlignedSequence> GetAlignedSequence(TextReader textReader)
{
bool isFilterRequired = IsFilterApplied();
bool display = true;
//Displays SAM as output.
string line = ReadNextLine(textReader);
while (line != null)
{
// Ignore headers.
if (!line.StartsWith(@"@", StringComparison.OrdinalIgnoreCase))
{
SAMAlignedSequence alignedSequence = SAMParser.ParseSequence(line);
if (isFilterRequired)
{
display = Filter(alignedSequence);
}
if (display)
{
yield return(alignedSequence);
}
}
line = ReadNextLine(textReader);
}
}
/// <summary>
/// Gets Aligned seqeunces in the Specified SAM file.
/// </summary>
/// <param name="textReader">SAM file stream.</param>
private IEnumerable <SAMAlignedSequence> GetAlignedSequence(MBFTextReader textReader)
{
bool isFilterRequired = IsFilterApplied();
bool display = true;
//Displays SAM as output.
while (textReader.HasLines)
{
SAMAlignedSequence alignedSequence = SAMParser.ParseSequence(textReader, false);
if (isFilterRequired)
{
display = Filter(alignedSequence);
}
if (display)
{
yield return(alignedSequence);
}
textReader.GoToNextLine();
}
}
